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Schneider H, Lai B, Krömer JO. Understanding the electron pathway fluidity of Synechocystis in biophotovoltaics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17225. [PMID: 39868486 PMCID: PMC11771661 DOI: 10.1111/tpj.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 10/07/2024] [Accepted: 12/13/2024] [Indexed: 01/28/2025]
Abstract
Biophotovoltaics offers a promising low-carbon footprint approach to utilize solar energy. It aims to couple natural oxygenic photosynthetic electrons to an external electron sink. This lays the foundation for a potentially high light-to-energy efficiency of the Biophotovoltaic process. However, there are still uncertainties around demonstrating the direct coupling of electron fluxes between photosystems and the external electrode. The dynamic cellular electron transfer network linked to physiological and environmental parameters poses a particular challenge here. In this work, the active cellular electron transfer network was modulated by tuning the cultivating conditions of Synechocystis and the operating conditions in Biophotovoltaics. The current output during darkness was found to be determined by the intracellular glycogen levels. Minimizing the intracellular glycogen pools also eliminated the dark-current output. Moreover, our results provide strong evidence that water splitting in photosystem II is the electron source enabling photocurrent, bypassing the microbe's metabolism. Eliminating the storage carbon as possible source of electrons did not reduce the specific photocurrent output, indicating an efficient coupling of photosynthetic electron flux to the anode. Furthermore, inhibiting respiration on the one hand increased the photocurrent and on the other hand showed a negative effect on the dark-current output. This suggested a switchable role of the respiratory electron transfer chain in the extracellular electron transfer pathway. Overall, we conclude that Synechocystis dynamically switches electron sources and utilizes different extracellular transfer pathways for the current output toward the external electron sink, depending on the physiological and environmental conditions.
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Affiliation(s)
- Hans Schneider
- Systems Biotechnology Group, Department Microbial BiotechnologyHelmholtz Centre for Environmental Research – UFZLeipzig04318Germany
| | - Bin Lai
- BMBF Junior Research Group Biophotovoltaics, Department Microbial BiotechnologyHelmholtz Centre for Environmental Research – UFZLeipzig04318Germany
| | - Jens O. Krömer
- Systems Biotechnology Group, Department Microbial BiotechnologyHelmholtz Centre for Environmental Research – UFZLeipzig04318Germany
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2
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Dmitrieva VA, Tyutereva EV, Voitsekhovskaja OV. What can reactive oxygen species (ROS) tell us about the action mechanism of herbicides and other phytotoxins? Free Radic Biol Med 2024; 220:92-110. [PMID: 38663829 DOI: 10.1016/j.freeradbiomed.2024.04.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024]
Abstract
Reactive oxygen species (ROS) are formed in plant cells continuously. When ROS production exceeds the antioxidant capacity of the cells, oxidative stress develops which causes damage of cell components and may even lead to the induction of programmed cell death (PCD). The levels of ROS production increase upon abiotic stress, but also during pathogen attack in response to elicitors, and upon application of toxic compounds such as synthetic herbicides or natural phytotoxins. The commercial value of many synthetic herbicides is based on weed death as result of oxidative stress, and for a number of them, the site and the mechanism of ROS production have been characterized. This review summarizes the current knowledge on ROS production in plants subjected to different groups of synthetic herbicides and natural phytotoxins. We suggest that the use of ROS-specific fluorescent probes and of ROS-specific marker genes can provide important information on the mechanism of action of these toxins. Furthermore, we propose that, apart from oxidative damage, elicitation of ROS-induced PCD is emerging as one of the important processes underlying the action of herbicides and phytotoxins.
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Affiliation(s)
- Valeria A Dmitrieva
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, 197022, Russia; Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Saint Petersburg, 196608, Russia
| | - Elena V Tyutereva
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, 197022, Russia
| | - Olga V Voitsekhovskaja
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, 197022, Russia.
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3
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de Pádua GMS, Pitteri TS, Ferreira Basso MA, de Vasconcelos LG, Ali A, Dall'Oglio EL, Sampaio OM, Curcino Vieira LC. Synthesis and Evaluation of New Phytotoxic Fluorinated Chalcones as Photosystem II and Seedling Growth Inhibitors. Chem Biodivers 2024; 21:e202301564. [PMID: 38373281 DOI: 10.1002/cbdv.202301564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 02/21/2024]
Abstract
The development of novel phytotoxic compounds has been an important aim of weed control research. In this study, we synthesized fluorinated chalcone derivatives featuring both electron-donating and electron-withdrawing groups. These compounds were evaluated both as inhibitors of the photosystem II (PSII) electron chain as well as inhibitors of the germination and seedling growth of Amaranthus plants. Chlorophyll a (Chl a) fluorescence assay was employed to evaluate their effects on PSII, while germination experiments were conducted to assess their impact on germination and seedling development. The results revealed promising herbicidal activity for (E)-3-(4-bromophenyl)-1-(4-fluorophenyl)prop-2-en-1-one (7 a) and (E)-1-(4-fluorophenyl)-3-phenylprop-2-en-1-one (7 e). Compounds 7 a and 7 e exhibited a reduction in Chl a parameters associated with performance indexes and electron transport per reaction center. This reduction suggests a decrease in PSII activity, attributed to the blockage of electron flow at the quinone pool. Molecular docking analyses of chalcone derivatives with the D1 protein of PSII revealed a stable binding conformation, wherein the carbonyl and fluorine groups interacted with Phe265 and His215 residues, respectively. Additionally, at a concentration of 100 μM, compound 7 e demonstrated pre- and post-emergent herbicidal activity, resulting in a reduction of the seed germination index, radicle and hypocotyl lengths of Amaranthus weeds.
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Affiliation(s)
| | - Taciane Santos Pitteri
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | | | | | - Akbar Ali
- Department of Chemistry, Government College University, Faisalabad, 38000, Pakistan
| | | | - Olívia Moreira Sampaio
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
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Traxler C, Gaines TA, Küpper A, Luemmen P, Dayan FE. The nexus between reactive oxygen species and the mechanism of action of herbicides. J Biol Chem 2023; 299:105267. [PMID: 37734554 PMCID: PMC10591016 DOI: 10.1016/j.jbc.2023.105267] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Herbicides are small molecules that act by inhibiting specific molecular target sites within primary plant metabolic pathways resulting in catastrophic and lethal consequences. The stress induced by herbicides generates reactive oxygen species (ROS), but little is known about the nexus between each herbicide mode of action (MoA) and their respective ability to induce ROS formation. Indeed, some herbicides cause dramatic surges in ROS levels as part of their primary MoA, whereas other herbicides may generate some ROS as a secondary effect of the stress they imposed on plants. In this review, we discuss the types of ROS and their respective reactivity and describe their involvement for each known MoA based on the new Herbicide Resistance Action Committee classification.
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Affiliation(s)
- Catherine Traxler
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anita Küpper
- Plant Biotechnology Division, Bayer CropScience, Chesterfield, Missouri, USA
| | - Peter Luemmen
- Research & Development Division, Bayer AG, Industriepark Höchst, Frankfurt am Main, Germany
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA.
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5
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Bogacz I, Doyle MD, Dobbek H, Zouni A, Messinger J, Yachandra VK, Kern JF, Yano J. Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function. PHOTOSYNTHESIS RESEARCH 2023; 158:91-107. [PMID: 37266800 PMCID: PMC10684718 DOI: 10.1007/s11120-023-01018-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 06/03/2023]
Abstract
One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the 'water wheel' to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421-425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831-15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).
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Affiliation(s)
- Rana Hussein
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany.
| | - Mohamed Ibrahim
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Holger Dobbek
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Athina Zouni
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, SE 75120, Uppsala, Sweden
- Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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6
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Fadeeva M, Klaiman D, Caspy I, Nelson N. Structure of Chlorella ohadii Photosystem II Reveals Protective Mechanisms against Environmental Stress. Cells 2023; 12:1971. [PMID: 37566050 PMCID: PMC10416949 DOI: 10.3390/cells12151971] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023] Open
Abstract
Green alga Chlorella ohadii is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This structure revealed 64 subunits, which encompassed 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, a unique subunit arrangement was observed to protect the oxygen-evolving complex. This arrangement involved PsbO (OEE1), PsbP (OEE2), PsbB, and PsbU (a homolog of plant OEE3). PsbU interacted with PsbO, PsbC, and PsbP, thereby stabilizing the shield of the oxygen-evolving complex. Significant changes were also observed at the stromal electron acceptor side. PsbY, identified as a transmembrane helix, was situated alongside PsbF and PsbE, which enclosed cytochrome b559. Supported by the adjacent C-terminal helix of Psb10, these four transmembrane helices formed a bundle that shielded cytochrome b559 from the surrounding solvent. Moreover, the bulk of Psb10 formed a protective cap, which safeguarded the quinone site and likely contributed to the stacking of PSII complexes. Based on our findings, we propose a protective mechanism that prevents QB (plastoquinone B) from becoming fully reduced. This mechanism offers insights into the regulation of electron transfer within PSII.
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Affiliation(s)
| | | | | | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (M.F.); (D.K.); (I.C.)
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7
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Kamada S, Nakajima Y, Shen JR. Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. J Biol Chem 2023:104839. [PMID: 37209822 PMCID: PMC10300377 DOI: 10.1016/j.jbc.2023.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone (PQ) molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with similar molecular structures to PQ can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95-2.10 Å resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site, and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone binding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII, and also provide information for the design of more efficient electron acceptors.
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Affiliation(s)
- Shinji Kamada
- Faculty of Science, Okayama University, Okayama 700-8503, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8503, Japan.
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8
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Fadeeva M, Klaiman D, Caspy I, Nelson N. CryoEM PSII structure reveals adaptation mechanisms to environmental stress in Chlorella ohadii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539358. [PMID: 37205566 PMCID: PMC10187303 DOI: 10.1101/2023.05.04.539358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Performing photosynthesis in the desert is a challenging task since it requires a fast adaptation to extreme illumination and temperature changes. To understand adaptive mechanisms, we purified Photosystem II (PSII) from Chlorella ohadii , a green alga from the desert soil surface, and identified structural elements that might enable the photosystem functioning under harsh conditions. The 2.72 Å cryogenic electron-microscopy (cryoEM) structure of PSII exhibited 64 subunits, encompassing 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, the oxygen evolving complex was protected by a unique subunit arrangement - PsbO (OEE1), PsbP (OEE2), CP47, and PsbU (plant OEE3 homolog). PsbU interacted with PsbO, CP43, and PsbP, thus stabilising the oxygen evolving shield. Substantial changes were observed on the stromal electron acceptor side - PsbY was identified as a transmembrane helix situated alongside PsbF and PsbE enclosing cytochrome b559, supported by the adjacent C-terminal helix of Psb10. These four transmembrane helices bundled jointly, shielding cytochrome b559 from the solvent. The bulk of Psb10 formed a cap protecting the quinone site and probably contributed to the PSII stacking. So far, the C. ohadii PSII structure is the most complete description of the complex, suggesting numerous future experiments. A protective mechanism that prevented Q B from rendering itself fully reduced is proposed.
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Affiliation(s)
| | | | - Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
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9
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Zhang X, Yang X, Huang Y, Hu J, Wu D, Yang N, Wang H. 2-Hydroxychalcone as a Novel Natural Photosynthesis Inhibitor against Bloom-Forming Cyanobacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15069-15079. [PMID: 36444958 DOI: 10.1021/acs.jafc.2c06665] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The control of harmful cyanobacterial blooms has been becoming a global challenge. The development of eco-friendly algicides with strong specificity is urgently needed. The photosynthetic apparatus is a promising target site for algicides to minimize the possible harmful effects on animals and humans. In this study, biologically derived 2-hydroxychalcone efficiently inhibited the growth of bloom-forming M. aeruginosa by selectively interfering with photosynthesis. 2-Hydroxychalcone targeting Photosystem II (PSII) inhibited electron transfer between the primary and secondary electron acceptors (QA and QB) and the binding of plastoquinone (PQ) molecules to the QB binding pocket at the acceptor side of PSII, as revealed by polyphasic chlorophyll (Chl) a fluorescence induction and QA- reoxidation kinetics. Molecular docking for 2-hydroxychalcone to D1 protein and the proteomic responses of M. aeruginosa suggested that 2-hydroxychalcone formed a stable monodentate ligand with the nonheme iron in D1 protein, provoking significant modulation of PSII proteins. The unique binding mode of 2-hydroxychalcone with PSII differentiated it from classical PSII inhibitors. Furthermore, 2-hydroxychalcone down-regulated the expression of microcystin (MC) synthesis-related genes to restrain MC synthesis and release. These results indicated the potential application of 2-hydroxychalcone as an algicide or a template scaffold for designing novel derivatives with superior algicidal activity.
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Affiliation(s)
- Xin Zhang
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
| | - Xu Yang
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
| | - Yichen Huang
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
| | - Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi710072, China
| | - Diao Wu
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
| | - Niu Yang
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
| | - Haiying Wang
- College of Life Sciences, South-Central Minzu University, Wuhan, Hubei430074, China
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10
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Soares LTXMG, Basso MAF, Dos Santos CMR, Ali A, Vasconcelos LG, Dall'Oglio EL, Sampaio OM, Vieira LCC. Binding Properties of Photosynthetic Herbicides: Photosynthetic Activity and Molecular Docking Approach towards 1,4-Dihydropyridines Derivatives. Chem Biodivers 2022; 19:e202200586. [PMID: 36383100 DOI: 10.1002/cbdv.202200586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
In the current work, we describe the synthesis of 1,4-dihydropyridine (1,4-DHP) derivatives via Hantzsch multicomponent reaction and their evaluation as photosystem II (PSII) inhibitors through chlorophyll a fluorescence bioassay. Among all the compounds tested, 1,1'-(2,4,6-trimethyl-1,4-dihydropyridine-3,5-diyl)bis(ethan-1-one) (4b) showed best results, reducing the parameters performance index on absorption basis (PIabs ) and electron transport per reaction center by 61 % and 49 %, respectively, as compared to the control. These results indicate the inhibitory activity of PSII over the electron transport chain. Additionally, a molecular docking approach using the protein D1 (PDB code 4V82) was performed in order to assess the structure-activity relationship among the 1,4-DHP derivatives over the PSII, which revealed that both, size of the group at position 4 and the carbonyl groups at the dihydropyridine ring are important for the ligand's interaction, particularly for the hydrogen-bonding interaction with the residues His215, Ser264, and Phe265. Thus, the optimization of these molecular features is the aim of our research group to extend the knowledge of PSII electron chain inhibitors and the establishment of new potent bioactive molecular scaffolds.
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Affiliation(s)
- Luís T X M G Soares
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | - Marcelo A F Basso
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | - Clarice M R Dos Santos
- Engineering Faculty, Federal University of Mato Grosso, Várzea Grande-MT, 78060-900, Brazil
| | - Akbar Ali
- Department of Chemistry, Government College University, Faisalabad, 38000, Pakistan
| | - Leonardo G Vasconcelos
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | - Evandro L Dall'Oglio
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | - Olívia M Sampaio
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
| | - Lucas C C Vieira
- Department of Chemistry, Federal University of Mato Grosso, Cuiabá-MT, 78060-900, Brazil
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11
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Ko SR, Jeong Y, Cho SH, Lee E, Jeong BS, Baek SH, Oh BH, Ahn CY, Oh HM, Cho BK, Cho S. Functional role of a novel algicidal compound produced by Pseudoruegeria sp. M32A2M on the harmful algae Alexandrium catenella. CHEMOSPHERE 2022; 300:134535. [PMID: 35405190 DOI: 10.1016/j.chemosphere.2022.134535] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
A marine phytoplankton dinoflagellate, Alexandrium sp. is known to cause worldwide harmful algal blooms, resulting in paralytic shellfish poisoning. In this study, we isolated a novel compound secreted by the marine bacterium Pseudoruegeria sp. M32A2M, and showed that it displays algicidal activity against A. catenella (group I). The molecular structure of the compound was analyzed by using 1H nuclear magnetic resonance (NMR), 13C NMR, and gas chromatography-mass spectrometry, which revealed that the compound was a diketopiperazine, cyclo[Ala-Gly]. Cyclo[Ala-Gly] induced a rapid decrease in the active chlorophyll a content and maximal quantum yield of photosystem II, leading to membrane disintegration after 24 h of its treatment. It showed the highest algicidal effect against diketopiperazines and also showed specific algicidal activities against several dinoflagellate species, but not for diatom species. In particular, cyclo[Ala-Gly] caused the transcriptional downregulation of the photosynthesis-related membrane complex in A. catenella, but not in the diatom Chaetoceros simplex. Based on structural modeling, we elucidated that cyclo[Ala-Gly] has a structure similar to that of plastoquinone, which transfers electrons by binding to the photosystem II core proteins PsbA and PsbD. This suggests a novel role for cyclo[Ala-Gly] as a potential inhibitor of photosynthesis.
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Affiliation(s)
- So-Ra Ko
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yujin Jeong
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang-Hyeok Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Eunju Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bo-Seong Jeong
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Seung Ho Baek
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology, Geoje, 53201, Republic of Korea
| | - Byung-Ha Oh
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Chi-Yong Ahn
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hee-Mock Oh
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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12
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Macromolecular conformational changes in photosystem II: interaction between structure and function. Biophys Rev 2022; 14:871-886. [DOI: 10.1007/s12551-022-00979-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/02/2022] [Indexed: 01/08/2023] Open
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13
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6-Ethoxy-4- N-(2-morpholin-4-ylethyl) -2-N-propan-2-yl-1,3, 5-triazine-2, 4-diamine endows herbicidal activity against Phalaris minor a weed of wheat crop field: An in -silico and experimental approaches of herbicide discovery. J Mol Model 2022; 28:77. [PMID: 35244782 DOI: 10.1007/s00894-021-05006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/14/2021] [Indexed: 10/18/2022]
Abstract
Phalaris minor is a major weed of wheat crop which has evolved resistance against herbicides. Isoproturon is the most accepted herbicide developed resistance in 1992. Later, introduced herbicides also developed resistance and cross-resistance to their respective binding sites. Isoproturon binds at the QB binding site of the D1 protein of photosystem-II (PS-II), which blocks the electron transfer in photosynthesis. In this work, we have carried out a series of computational studies to prioritize the promising herbicides against D1 protein of P. minor. Through the computational studies, twenty-four lead molecules are prioritized which have shown a higher binding affinity and inhibition constant than the reference ligand molecule. The binding and conformational stability of docked complexes was evaluated by molecular dynamics simulations and binding free energy calculations i.e., MM/PBSA. A list of amino acids such as Ala225, Ser226, Phe227, and Asn229 present in the binding site of protein is obtained to be playing an important role in the stability of the protein-lead complex via hydrogen bond and π-π interactions. Binding free energy calculation revealed that the selected lead molecule binding is energetically favorable and driven by electrostatic interactions. Among 24 leads, computational results have uncovered eight promising compounds as potential herbicides which have shown comparable physiochemical profile, better docking scores, system stability, H-bond occupancy, and binding free energy than terbutryn, a reference molecule. These prioritized molecules were custom synthesized and evaluated for their herbicidal activity and specificity through whole plant assay under laboratory-controlled conditions. The lead molecule ELC5 (6-ethoxy-4-N-(2-morpholin-4-ylethyl)-2-N-propan-2-yl-1,3,5-triazine-2,4-diamine) has shown comparable activity to the reference herbicide(isoproturon) against P. minor.
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14
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Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proc Natl Acad Sci U S A 2022; 119:e2116765118. [PMID: 34937700 PMCID: PMC8740770 DOI: 10.1073/pnas.2116765118] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
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Affiliation(s)
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, CT 06520
| | | | - M R Gunner
- Department of Physics, City College of New York, New York, NY 100031
| | | | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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15
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J. Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition. Nat Commun 2021; 12:6531. [PMID: 34764256 PMCID: PMC8585918 DOI: 10.1038/s41467-021-26781-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.
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Affiliation(s)
- Rana Hussein
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mohamed Ibrahim
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Asmit Bhowmick
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Philipp S. Simon
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Ruchira Chatterjee
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Louise Lassalle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Margaret Doyle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Isabel Bogacz
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - In-Sik Kim
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Mun Hon Cheah
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Sheraz Gul
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Casper de Lichtenberg
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden ,grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Petko Chernev
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Cindy C. Pham
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Iris D. Young
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sergio Carbajo
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Franklin D. Fuller
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Roberto Alonso-Mori
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Alex Batyuk
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Kyle D. Sutherlin
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aaron S. Brewster
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Robert Bolotovsky
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Derek Mendez
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - James M. Holton
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Nigel W. Moriarty
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Uwe Bergmann
- grid.14003.360000 0001 2167 3675Department of Physics, University of Wisconsin–Madison, Madison, WI 53706 USA
| | - Nicholas K. Sauter
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Holger Dobbek
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120, Uppsala, Sweden. .,Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden.
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Vittal K. Yachandra
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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16
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Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum. THE ISME JOURNAL 2021; 15:3384-3398. [PMID: 34054125 PMCID: PMC8528915 DOI: 10.1038/s41396-021-01015-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 02/03/2023]
Abstract
Photoferrotrophy allows anoxygenic phototrophs to use reduced iron as an electron donor for primary productivity. Recent work shows that freshwater photoferrotrophs can use electrons from solid-phase conductive substances via phototrophic extracellular electron uptake (pEEU), and the two processes share the underlying electron uptake mechanism. However, the ability of marine phototrophs to perform photoferrotrophy and pEEU, and the contribution of these processes to primary productivity is largely unknown. To fill this knowledge gap, we isolated 15 new strains of the marine anoxygenic phototroph Rhodovulum sulfidophilum on electron donors such as acetate and thiosulfate. We observed that all of the R. sulfidophilum strains isolated can perform photoferrotrophy. We chose strain AB26 as a representative strain to study further, and find that it can also perform pEEU from poised electrodes. We show that during pEEU, AB26 transfers electrons to the photosynthetic electron transport chain. Furthermore, systems biology-guided mutant analysis shows that R. sulfidophilum AB26 uses a previously unknown diheme cytochrome c protein, which we call EeuP, for pEEU but not photoferrotrophy. Homologs of EeuP occur in a range of widely distributed marine microbes. Overall, these results suggest that photoferrotrophy and pEEU contribute to the biogeochemical cycling of iron and carbon in marine ecosystems.
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17
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Battaglino B, Grinzato A, Pagliano C. Binding Properties of Photosynthetic Herbicides with the Q B Site of the D1 Protein in Plant Photosystem II: A Combined Functional and Molecular Docking Study. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081501. [PMID: 34451546 PMCID: PMC8398153 DOI: 10.3390/plants10081501] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 05/07/2023]
Abstract
Photosystem II (PSII) is a multi-subunit enzymatic complex embedded in the thylakoid membranes responsible for the primary photosynthetic reactions vital for plants. Many herbicides used for weed control inhibit PSII by interfering with the photosynthetic electron transport at the level of the D1 protein, through competition with the native plastoquinone for the QB site. Molecular details of the interaction of these herbicides in the D1 QB site remain to be elucidated in plants. Here, we investigated the inhibitory effect on plant PSII of the PSII-inhibiting herbicides diuron, metobromuron, bentazon, terbuthylazine and metribuzin. We combined analysis of OJIP chlorophyll fluorescence kinetics and PSII activity assays performed on thylakoid membranes isolated from pea plants with molecular docking using the high-resolution PSII structure recently solved from the same plant. Both approaches showed for terbuthylazine, metribuzin and diuron the highest affinity for the D1 QB site, with the latter two molecules forming hydrogen bonds with His215. Conversely, they revealed for bentazon the lowest PSII inhibitory effect accompanied by a general lack of specificity for the QB site and for metobromuron an intermediate behavior. These results represent valuable information for future design of more selective herbicides with enhanced QB binding affinities to be effective in reduced amounts.
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Affiliation(s)
- Beatrice Battaglino
- Applied Science and Technology Department—BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy;
| | - Alessandro Grinzato
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58 B, 35121 Padova, Italy;
| | - Cristina Pagliano
- Applied Science and Technology Department—BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy;
- Correspondence: ; Tel.: +39-0110904626
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18
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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19
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Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213183] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Zhang Y, Calabrese EJ, Zhang J, Gao D, Qin M, Lin Z. A trigger mechanism of herbicides to phytoplankton blooms: From the standpoint of hormesis involving cytochrome b 559, reactive oxygen species and nitric oxide. WATER RESEARCH 2020; 173:115584. [PMID: 32062224 DOI: 10.1016/j.watres.2020.115584] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
The cause of phytoplankton blooms has been extensively discussed and largely attributed to favorable external conditions such as nitrogen/phosphorus resources, pH and temperature. Here from the standpoint of hormesis response, we propose that phytoplankton blooms are initiated by stimulatory effects of low concentrations of herbicides as environmental contaminants spread over estuaries and lakes. The experimental results revealed general stimulations by herbicides on Microcystis aeruginosa and Selenastrum capricornutum, with the maximum stimulation in the 30-60% range, depending on the agent and experiment. In parallel with enhancing stimulation, the ratio of HP (high-potential) form to LP (low-potential) form of cytochrome b559 (RHL) was observed decreasing, while intracellular reactive oxygen species (ROS) were observed increasing. We propose that the ROS originated from the thermodynamic transformation of cytochrome b559, enhancing the stimulatory response. Furthermore, the results also proved that thermodynamic states of cytochrome b559 could be modulated by nitric oxide, thus affecting cellular equilibrium of oxidative stress (OS) and correspondingly causing the inhibitory effect of higher concentrations of herbicides on phytoplankton. This suggests that hormesis substantially derives from equilibrium shifting of OS. Moreover, it is reasonable to infer that phytoplankton blooms would be motivated by herbicides or other environmental pollutants. This study provides a new thought into global phytoplankton blooms from a contaminant perspective.
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Affiliation(s)
- Yueheng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Edward J Calabrese
- Department of Public Health, Environmental Health Sciences, Morrill I, N344, University of Massachusetts, Amherst, MA, 01003, USA
| | - Junyi Zhang
- Wuxi Environmental Monitoring Centre, Jiangsu, China
| | - Dan Gao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Mengnan Qin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.
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21
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Swatch GK, Singh DP, Khattar JS, Mohapatra PK. Interaction of pretilachlor with PS-II activity of the cyanobacterium Desmonostoc muscorum PUPCCC 405.10. J Basic Microbiol 2020; 60:532-542. [PMID: 32159865 DOI: 10.1002/jobm.201900706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/26/2020] [Indexed: 11/10/2022]
Abstract
Interaction of pretilachlor with photosystem (PS)-II of the cyanobacterium Desmonostoc muscorum PUPCCC 405.10 has been studied in this paper. Pretilachlor negatively affected growth, chlorophyll a (Chl a), photosynthesis, and carbon dissimilation in a dose-dependent manner. Effects were also observed in PSs, especially PS-II (an 11-35% decrease), as well as the whole photosynthetic electron transport activity. The fluorescence emission spectrum of Chl a revealed a dose-dependent effect of pretilachlor on both the antenna and the core complex of PSs, with more severe effect on the former. Data of O-J-I-P fluorescence transient of Chl a revealed that pretilachlor interfered with electron flow between QA and QB sites of PS-II. It was further observed that pretilachlor decreased maximum fluorescence, variable and relative variable fluorescence, maximum quantum yield, quantum yield of electron transport, the rate of trapped exciton movement, quantum yield of electron transfer, and performance index of primary photochemistry; however, there was a progressive increase in the net rate of PS-II closure, quantum yield of energy dissipation, and effective antenna size per active reaction center. A decrease in photosynthetic activity leads to a decrease in carbon dissimilation, as evidenced by low activity of glucose-6-phosphate dehydrogenase and pyruvate kinase. Thus, pretilachlor, which is otherwise known to kill weeds by interfering with cell division, affected the growth of the cyanobacteria by interacting with PS-II.
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22
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The study of conformational changes in photosystem II during a charge separation. J Mol Model 2020; 26:75. [PMID: 32152736 DOI: 10.1007/s00894-020-4332-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/23/2020] [Indexed: 12/14/2022]
Abstract
Photosystem II (PSII) is a multi-subunit pigment-protein complex and is one of several protein assemblies that function cooperatively in photosynthesis in plants and cyanobacteria. As more structural data on PSII become available, new questions arise concerning the nature of the charge separation in PSII reaction center (RC). The crystal structure of PSII RC from cyanobacteria Thermosynechococcus vulcanus was selected for the computational study of conformational changes in photosystem II associated to the charge separation process. The parameterization of cofactors and lipids for classical MD simulation with Amber force field was performed. The parametrized complex of PSII was embedded in the lipid membrane for MD simulation with Amber in Gromacs. The conformational behavior of protein and the cofactors directly involved in the charge separation were studied by MD simulations and QM/MM calculations. This study identified the most likely mechanism of the proton-coupled reduction of plastoquinone QB. After the charge separation and the first electron transfer to QB, the system undergoes conformational change allowing the first proton transfer to QB- mediated via Ser264. After the second electron transfer to QBH, the system again adopts conformation allowing the second proton transfer to QBH-. The reduced QBH2 would then leave the binding pocket.
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23
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Cardona T, Rutherford AW. Evolution of Photochemical Reaction Centres: More Twists? TRENDS IN PLANT SCIENCE 2019; 24:1008-1021. [PMID: 31351761 DOI: 10.1016/j.tplants.2019.06.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 05/27/2023]
Abstract
One of the earliest events in the molecular evolution of photosynthesis is the structural and functional specialisation of type I (ferredoxin-reducing) and type II (quinone-reducing) reaction centres. In this opinion article we point out that the homodimeric type I reaction centre of heliobacteria has a calcium-binding site with striking structural similarities to the Mn4CaO5 cluster of photosystem II. These similarities indicate that most of the structural elements required to evolve water oxidation chemistry were present in the earliest reaction centres. We suggest that the divergence of type I and type II reaction centres was made possible by a drastic structural shift linked to a change in redox properties that coincided with or facilitated the origin of photosynthetic water oxidation.
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Affiliation(s)
- Tanai Cardona
- Imperial College London, Department of Life Sciences, London, UK. @imperial.ac.uk
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Bak A, Pizova H, Kozik V, Vorcakova K, Kos J, Treml J, Odehnalova K, Oravec M, Imramovsky A, Bobal P, Smolinski A, Trávníček Z, Jampilek J. SAR-mediated Similarity Assessment of the Property Profile for New, Silicon-Based AChE/BChE Inhibitors. Int J Mol Sci 2019; 20:E5385. [PMID: 31671776 PMCID: PMC6862691 DOI: 10.3390/ijms20215385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 12/20/2022] Open
Abstract
A set of 25 novel, silicon-based carbamate derivatives as potential acetyl- and butyrylcholinesterase (AChE/BChE) inhibitors was synthesized and characterized by their in vitro inhibition profiles and the selectivity indexes (SIs). The prepared compounds were also tested for their inhibition potential on photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. In fact, some of the newly prepared molecules revealed comparable or even better inhibitory activities compared to the marketed drugs (rivastigmine or galanthamine) and commercially applied pesticide Diuron®, respectively. Generally, most compounds exhibited better inhibition potency towards AChE; however, a wider activity span was observed for BChE. Notably, benzyl N-[(1S)-2-[(tert-butyldimethylsilyl)oxy]-1-[(2-hydroxyphenyl)carbamoyl]ethyl]-carbamate (2) and benzyl N-[(1S)-2-[(tert-butyldimethylsilyl)oxy]-1-[(3-hydroxyphenyl)carbamoyl]ethyl]-carbamate (3) were characterized by fairly high selective indexes. Specifically, compound 2 was prescribed with the lowest IC50 value that corresponds quite well with galanthamine inhibition activity, while the inhibitory profiles of molecules 3 and benzyl-N-[(1S)-2-[(tert-butyldimethylsilyl)oxy]-1-[(4-hydroxyphenyl)carbamoyl]ethyl]carbamate (4) are in line with rivastigmine activity. Moreover, a structure-activity relationship (SAR)-driven similarity evaluation of the physicochemical properties for the carbamates examined appeared to have foreseen the activity cliffs using a similarity-activity landscape index for BChE inhibitory response values. The 'indirect' ligand-based and 'direct' protein-mediated in silico approaches were applied to specify electronic/steric/lipophilic factors that are potentially valid for quantitative (Q)SAR modeling of the carbamate analogues. The stochastic model validation was used to generate an 'average' 3D-QSAR pharmacophore pattern. Finally, the target-oriented molecular docking was employed to (re)arrange the spatial distribution of the ligand property space for BChE and photosystem II (PSII).
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Affiliation(s)
- Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland.
| | - Hana Pizova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 612 42 Brno, Czech Republic.
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland.
| | - Katarina Vorcakova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic.
| | - Jiri Kos
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic, (J.K.).
| | - Jakub Treml
- Department of Molecular Biology and Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 612 42 Brno, Czech Republic.
| | - Klara Odehnalova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 612 42 Brno, Czech Republic.
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, 60300 Brno, Czech Republic.
| | - Ales Imramovsky
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic.
| | - Pavel Bobal
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 612 42 Brno, Czech Republic.
| | - Adam Smolinski
- Department of Energy Saving and Air Protection, Central Mining Institute, Plac Gwarkow 1, 40 166 Katowice, Poland.
| | - Zdeněk Trávníček
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic, (J.K.).
| | - Josef Jampilek
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic, (J.K.).
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Thiour-Mauprivez C, Martin-Laurent F, Calvayrac C, Barthelmebs L. Effects of herbicide on non-target microorganisms: Towards a new class of biomarkers? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:314-325. [PMID: 31153078 DOI: 10.1016/j.scitotenv.2019.05.230] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 05/19/2023]
Abstract
Conventional agriculture still relies on the general use of agrochemicals (herbicides, fungicides and insecticides) to control various pests (weeds, fungal pathogens and insects), to ensure the yield of crop and to feed a constantly growing population. The generalized use of pesticides in agriculture leads to the contamination of soil and other connected environmental resources. The persistence of pesticide residues in soil is identified as a major threat for in-soil living organisms that are supporting an important number of ecosystem services. Although authorities released pesticides on the market only after their careful and thorough evaluation, the risk assessment for in-soil living organisms is unsatisfactory, particularly for microorganisms for which pesticide toxicity is solely considered by one global test measuring N mineralization. Recently, European Food Safety Authority (EFSA) underlined the lack of standardized methods to assess pesticide ecotoxicological effects on soil microorganisms. Within this context, there is an obvious need to develop innovative microbial markers sensitive to pesticide exposure. Biomarkers that reveal direct effects of pesticides on microorganisms are often viewed as the panacea. Such biomarkers can only be developed for pesticides having a mode of action inhibiting a specific enzyme not only found in the targeted organisms but also in microorganisms which are considered as "non-target organisms" by current regulations. This review explores possible ways of innovation to develop such biomarkers for herbicides. We scanned the herbicide classification by considering the mode of action, the targeted enzyme and the ecotoxicological effects of each class of active substance in order to identify those that can be tracked using sensitive microbial markers.
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Affiliation(s)
- Clémence Thiour-Mauprivez
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21065 Dijon, France
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21065 Dijon, France
| | - Christophe Calvayrac
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650 Banyuls-sur-Mer, France.
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26
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Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL. Triazine Probes Target Ascorbate Peroxidases in Plants. PLANT PHYSIOLOGY 2019; 180:1848-1859. [PMID: 31138623 PMCID: PMC6670103 DOI: 10.1104/pp.19.00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Though they are rare in nature, anthropogenic 1,3,5-triazines have been used in herbicides as chemically stable scaffolds. Here, we show that small 1,3,5-triazines selectively target ascorbate peroxidases (APXs) in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), liverwort (Marchantia polymorpha), and other plant species. The alkyne-tagged 2-chloro-4-methyl-1,3,5-triazine probe KSC-3 selectively binds APX enzymes, both in crude extracts and in living cells. KSC-3 blocks APX activity, thereby reducing photosynthetic activity under moderate light stress, even in apx1 mutant plants. This suggests that APX enzymes in addition to APX1 protect the photosystem against reactive oxygen species. Profiling APX1 with KCS-3 revealed that the catabolic products of atrazine (a 1,3,5-triazine herbicide), which are common soil pollutants, also target APX1. Thus, KSC-3 is a powerful chemical probe to study APX enzymes in the plant kingdom.
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Affiliation(s)
- Kyoko Morimoto
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Kyle S Cole
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Collin H Witt
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Daniel Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Daniel Krahn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Monika Stegmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Farnusch Kaschani
- Zentrum für Medizinische Biotechnologie, Chemical Biology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Markus Kaiser
- Zentrum für Medizinische Biotechnologie, Chemical Biology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonathan Burton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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Kaminskaya OP, Shuvalov VA. Analysis of the transformation effect in cytochrome b559 of photosystem II in terms of the model of the heme-quinone redox interaction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1161-1172. [PMID: 32314739 DOI: 10.1016/j.bbabio.2018.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Transformation of three-component redox pattern of cytochrome (Cyt) b559 in PS II membrane fragments upon various treatments is manifested in decrease of the relative content (R) of the high potential (HP) redox form of Cyt b559 and concomitant increase in the fractions of the two lower potential forms. Redox titration of Cyt b559 in different types of PS II membrane preparations was performed and revealed that (1) alteration of redox titration curve of Cyt b559 upon treatment of a sample is not specific to the type of treatment; (2) each value of RHP defines the individual shape of the redox titration curve; (3) population of Cyt b559 may exist in several stable forms with multicomponent redox pattern: three types of three-component redox pattern and one type of two-component redox pattern as well as in the form with a single Em; (4) transformation of Cyt b559 proceeds as successive conversion between the stable forms with multicomponent redox pattern; (5) upon harsh treatments, Cyt b559 abruptly converts into the state with a single Em which value is intermediate between the Em values of the two lower potential forms. Analysis of the data using the model of Cyt b559-quinone redox interaction revealed that diminution of RHP in a range from 80 to 10% reflects a shift in redox equilibrium between the heme group of Cyt b559 and the interacting quinone, due to a gradual decrease of 90 mV in Em of the heme group at the virtually unchanged Em of the quinone component.
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Affiliation(s)
- Olga P Kaminskaya
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
| | - Vladimir A Shuvalov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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28
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Nain-Perez A, Barbosa LCA, Maltha CRA, Giberti S, Forlani G. Tailoring Natural Abenquines To Inhibit the Photosynthetic Electron Transport through Interaction with the D1 Protein in Photosystem II. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:11304-11311. [PMID: 29191002 DOI: 10.1021/acs.jafc.7b04624] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Abenquines are natural N-acetylaminobenzoquinones bearing amino acid residues, which act as weak inhibitors of the photosynthetic electron transport chain. Aiming to exploit the abenquine scaffold as a model for the synthesis of new herbicides targeting photosynthesis, 14 new analogues were prepared by replacing the amino acid residue with benzylamines and the acetyl with different acyl groups. The synthesis was accomplished in three steps with a 68-95% overall yield from readily available 2,5-dimethoxyaniline, acyl chlorides, and benzyl amines. Key steps include (i) acylation of the aniline, (ii) oxidation, and (iii) oxidative addition of the benzylamino moiety. The compounds were assayed for their activity as Hill inhibitors, under basal, uncoupled, or phosphorylating conditions, or excluding photosystem I. Four analogues showed high effectiveness (IC50 = 0.1-0.4 μM), comparable with the commercial herbicide diuron (IC50 = 0.3 μM). The data suggest that this class of compounds interfere at the reducing side of photosystem II, having protein D1 as the most probable target. Molecular docking studies with the plastoquinone binding site of Spinacia oleracea further strengthened this proposal.
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Affiliation(s)
- Amalyn Nain-Perez
- Department of Chemistry, Universidade Federal de Minas Gerais , Av. Pres. Antônio Carlos, 6627, Campus Pampulha, CEP 31270-901, Belo Horizonte, MG Brazil
| | - Luiz C A Barbosa
- Department of Chemistry, Universidade Federal de Minas Gerais , Av. Pres. Antônio Carlos, 6627, Campus Pampulha, CEP 31270-901, Belo Horizonte, MG Brazil
- Department of Chemistry, Universidade Federal de Viçosa , Viçosa, Av. P. H. Rolfs s/n, CEP 36570-000, Viçosa, MG Brazil
| | - Celia R A Maltha
- Department of Chemistry, Universidade Federal de Viçosa , Viçosa, Av. P. H. Rolfs s/n, CEP 36570-000, Viçosa, MG Brazil
| | - Samuele Giberti
- Department of Life Science and Biotechnology, University of Ferrara , via L. Borsari 46, I-44121 Ferrara, Italy
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of Ferrara , via L. Borsari 46, I-44121 Ferrara, Italy
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29
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Siddiq MA, Hochberg GK, Thornton JW. Evolution of protein specificity: insights from ancestral protein reconstruction. Curr Opin Struct Biol 2017; 47:113-122. [PMID: 28841430 PMCID: PMC6141201 DOI: 10.1016/j.sbi.2017.07.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/13/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Specific interactions between proteins and their molecular partners drive most biological processes, so understanding how these interactions evolve is an important question for biochemists and evolutionary biologists alike. It is often thought that ancestral proteins were systematically more promiscuous than modern proteins and that specificity usually evolves after gene duplication by partitioning and refining the activities of multifunctional ancestors. However, recent studies using ancestral protein reconstruction (APR) have found that ligand-specific functions in some modern protein families evolved de novo from ancestors that did not already have those functions. Further, the new specific interactions evolved by simple mechanisms, with just a few mutations changing classically recognized biochemical determinants of specificity, such as steric and electrostatic complementarity. Acquiring new specific interactions during evolution therefore appears to be neither difficult nor rare. Rather, it is likely that proteins continually gain and lose new activities over evolutionary time as mutations cause subtle but consequential changes in the shape and electrostatics of interaction interfaces. Only a few of these activities, however, are incorporated into the biological processes that contribute to fitness before they are lost to the ravages of further mutation.
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Affiliation(s)
| | | | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, USA; Department of Human Genetics, University of Chicago, USA.
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30
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Funar-Timofei S, Borota A, Crisan L. Combined molecular docking and QSAR study of fused heterocyclic herbicide inhibitors of D1 protein in photosystem II of plants. Mol Divers 2017; 21:437-454. [DOI: 10.1007/s11030-017-9735-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
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31
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Najafpour MM, Moghaddam NJ, Hosseini SM, Madadkhani S, Hołyńska M, Mehrabani S, Bagheri R, Song Z. Nanolayered manganese oxides: insights from inorganic electrochemistry. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00215g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electrochemistry of nanolayered Mn oxides in the presence of LiClO4 at pH = 6.3 under different conditions was studied.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
- Center of Climate Change and Global Warming
| | - Navid Jameei Moghaddam
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | | | - Sepideh Madadkhani
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | - Małgorzata Hołyńska
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW)
- Philipps-Universität Marburg
- D-35032 Marburg
- Germany
| | - Somayeh Mehrabani
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
| | - Robabeh Bagheri
- Surface Protection Research Group
- Surface Department
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo 315201
| | - Zhenlun Song
- Surface Protection Research Group
- Surface Department
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo 315201
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32
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Senge MO, MacGowan SA, O'Brien JM. Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles. Chem Commun (Camb) 2016; 51:17031-63. [PMID: 26482230 DOI: 10.1039/c5cc06254c] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.
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Affiliation(s)
- Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland and Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
| | - Stuart A MacGowan
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Jessica M O'Brien
- Medicinal Chemistry, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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Abstract
To what extent is the convergent evolution of protein function attributable to convergent or parallel changes at the amino acid level? The mutations that contribute to adaptive protein evolution may represent a biased subset of all possible beneficial mutations owing to mutation bias and/or variation in the magnitude of deleterious pleiotropy. A key finding is that the fitness effects of amino acid mutations are often conditional on genetic background. This context dependence (epistasis) can reduce the probability of convergence and parallelism because it reduces the number of possible mutations that are unconditionally acceptable in divergent genetic backgrounds. Here, I review factors that influence the probability of replicated evolution at the molecular level.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
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Kasuno M, Kimura H, Yasutomo H, Torimura M, Murakami D, Tsukatani Y, Hanada S, Matsushita T, Tao H. An Evaluation of Sensor Performance for Harmful Compounds by Using Photo-Induced Electron Transfer from Photosynthetic Membranes to Electrodes. SENSORS 2016; 16:438. [PMID: 27023553 PMCID: PMC4850952 DOI: 10.3390/s16040438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 11/16/2022]
Abstract
Rapid, simple, and low-cost screening procedures are necessary for the detection of harmful compounds in the effluent that flows out of point sources such as industrial outfall. The present study investigated the effects on a novel sensor of harmful compounds such as KCN, phenol, and herbicides such as 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), 2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine (atrazine), and 2-N-tert-butyl-4-N-ethyl-6-methylsulfanyl-1,3,5-triazine-2,4-diamine (terbutryn). The sensor employed an electrode system that incorporated the photocurrent of intra-cytoplasmic membranes (so-called chromatophores) prepared from photosynthetic bacteria and linked using carbon paste electrodes. The amperometric curve (photocurrent-time curve) of photo-induced electron transfer from chromatophores of the purple photosynthetic bacterium Rhodobacter sphaeroides to the electrode via an exogenous electron acceptor was composed of two characteristic phases: an abrupt increase in current immediately after illumination (I₀), and constant current over time (Ic). Compared with other redox compounds, 2,5-dichloro-1,4-benzoquinone (DCBQ) was the most useful exogenous electron acceptor in this system. Photo-reduction of DCBQ exhibited Michaelis-Menten-like kinetics, and reduction rates were dependent on the amount of DCBQ and the photon flux intensity. The Ic decreased in the presence of KCN at concentrations over 0.05 μM (=μmol·dm(-3)). The I₀ decreased following the addition of phenol at concentrations over 20 μM. The Ic was affected by terbutryn at concentrations over 10 μM. In contrast, DCMU and atrazine had no effect on either I₀ or Ic. The utility of this electrode system for the detection of harmful compounds is discussed.
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Affiliation(s)
- Megumi Kasuno
- Department of Materials Chemistry, Faculty of Science and Technology, Ryukoku University, Otsu, Shiga 520-2194, Japan.
| | - Hiroki Kimura
- Department of Materials Chemistry, Faculty of Science and Technology, Ryukoku University, Otsu, Shiga 520-2194, Japan.
| | - Hisataka Yasutomo
- Department of Materials Chemistry, Faculty of Science and Technology, Ryukoku University, Otsu, Shiga 520-2194, Japan.
| | - Masaki Torimura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan.
| | - Daisuke Murakami
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan.
| | - Yusuke Tsukatani
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Satoshi Hanada
- Institute for Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
| | - Takayuki Matsushita
- Department of Materials Chemistry, Faculty of Science and Technology, Ryukoku University, Otsu, Shiga 520-2194, Japan.
| | - Hiroaki Tao
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan.
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Abstract
Herein we report that the reaction of KMnO4 with cobalt nanoparticles coated with multiple graphene layers forms a promising catalyst toward water oxidation. The compound was characterized by scanning electron microscopy, energy-dispersive spectroscopy, high resolution transmission electron microscopy, X-ray diffraction, electronic spectroscopy, Fourier transform infrared spectroscopy, and atomic absorption spectroscopy. In addition to the Mn oxide-based characteristics of the catalyst, it is a conductive, self-healing, recycling, highly dispersible, magnetically separable, environmentally friendly, and nano-sized catalyst for water oxidation. The turnover frequency for the catalyst toward water oxidation is 0.1 and 0.05 (mmol O2 per mol Mn s) in the presence of cerium(iv) ammonium nitrate and photo-produced Ru(bpy)3(3+).
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
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36
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Bricker TM, Mummadisetti MP, Frankel LK. Recent advances in the use of mass spectrometry to examine structure/function relationships in photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:227-46. [PMID: 26390944 DOI: 10.1016/j.jphotobiol.2015.08.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 01/24/2023]
Abstract
Tandem mass spectrometry often coupled with chemical modification techniques, is developing into increasingly important tool in structural biology. These methods can provide important supplementary information concerning the structural organization and subunit make-up of membrane protein complexes, identification of conformational changes occurring during enzymatic reactions, identification of the location of posttranslational modifications, and elucidation of the structure of assembly and repair complexes. In this review, we will present a brief introduction to Photosystem II, tandem mass spectrometry and protein modification techniques that have been used to examine the photosystem. We will then discuss a number of recent case studies that have used these techniques to address open questions concerning PS II. These include the nature of subunit-subunit interactions within the phycobilisome, the interaction of phycobilisomes with Photosystem I and the Orange Carotenoid Protein, the location of CyanoQ, PsbQ and PsbP within Photosystem II, and the identification of phosphorylation and oxidative modification sites within the photosystem. Finally, we will discuss some of the future prospects for the use of these methods in examining other open questions in PS II structural biochemistry.
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Affiliation(s)
- Terry M Bricker
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Manjula P Mummadisetti
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
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37
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Najafpour MM, Abasi M, Tomo T, Allakhverdiev SI. Nanolayered manganese oxide/C(60) composite: a good water-oxidizing catalyst for artificial photosynthetic systems. Dalton Trans 2015; 43:12058-64. [PMID: 24984108 DOI: 10.1039/c4dt00599f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
For the first time, we considered Mn oxide/C60 composites as water-oxidizing catalysts. The composites were synthesized by easy and simple procedures, and characterized by some methods. The water-oxidizing activities of these composites were also measured in the presence of cerium(iv) ammonium nitrate. We found that the nanolayered Mn oxide/C60 composites show promising activity toward water oxidation.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
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38
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Lambreva MD, Russo D, Polticelli F, Scognamiglio V, Antonacci A, Zobnina V, Campi G, Rea G. Structure/function/dynamics of photosystem II plastoquinone binding sites. Curr Protein Pept Sci 2015; 15:285-95. [PMID: 24678671 PMCID: PMC4030317 DOI: 10.2174/1389203715666140327104802] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 11/22/2013] [Accepted: 03/16/2014] [Indexed: 11/22/2022]
Abstract
Photosystem II (PSII)
continuously attracts the attention of researchers aiming to unravel the riddle
of its functioning and efficiency fundamental for all life on Earth. Besides, an
increasing number of biotechnological applications have been envisaged
exploiting and mimicking the unique properties of this macromolecular
pigment-protein complex. The PSII organization and working principles have
inspired the design of electrochemical water splitting schemes and charge
separating triads in energy storage systems as well as biochips and sensors for
environmental, agricultural and industrial screening of toxic compounds. An
intriguing opportunity is the development of sensor devices, exploiting native
or manipulated PSII complexes or ad hoc synthesized polypeptides
mimicking the PSII reaction centre proteins as bio-sensing elements. This review
offers a concise overview of the recent improvements in the understanding of
structure and function of PSII donor side, with focus on the interactions of the
plastoquinone cofactors with the surrounding environment and operational
features. Furthermore, studies focused on photosynthetic proteins
structure/function/dynamics and computational analyses aimed at rational design
of high-quality bio-recognition elements in biosensor devices are discussed.
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Affiliation(s)
| | | | | | | | | | | | | | - Giuseppina Rea
- Institute of Crystallography, National Research Council, Monterotondo, Italy.
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39
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Najafpour MM, Fekete M, Sedigh DJ, Aro EM, Carpentier R, Eaton-Rye JJ, Nishihara H, Shen JR, Allakhverdiev SI, Spiccia L. Damage Management in Water-Oxidizing Catalysts: From Photosystem II to Nanosized Metal Oxides. ACS Catal 2015. [DOI: 10.1021/cs5015157] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Monika Fekete
- School of Chemistry and the ARC Centre of Excellence for Electromaterials Science, Monash University, Victoria 3800, Australia
| | | | - Eva-Mari Aro
- Department of Biochemistry and Food Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Robert Carpentier
- Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Julian J. Eaton-Rye
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Hiroshi Nishihara
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Suleyman I. Allakhverdiev
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
- Department of Plant Physiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119991, Russia
| | - Leone Spiccia
- School of Chemistry and the ARC Centre of Excellence for Electromaterials Science, Monash University, Victoria 3800, Australia
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40
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Najafpour MM, Hosseini SM, Hołyńska M, Tomo T, Allakhverdiev SI. Gold nanorods or nanoparticles deposited on layered manganese oxide: new findings. NEW J CHEM 2015. [DOI: 10.1039/c5nj01392e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our results show that nano-sized gold has no significant effect on the water-oxidation activity of the Mn oxide phase in the presence of Ce(iv).
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
- Center of Climate Change and Global Warming
| | | | - Małgorzata Hołyńska
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW)
- Philipps-Universität Marburg
- D-35032 Marburg
- Germany
| | - Tatsuya Tomo
- Department of Biology
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601
- Japan
| | - Suleyman I. Allakhverdiev
- Controlled Photobiosynthesis Laboratory
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow 127276
- Russia
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41
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Najafpour MM, Amini E. Nano-sized Mn oxides on halloysite or high surface area montmorillonite as efficient catalysts for water oxidation with cerium(iv) ammonium nitrate: support from natural sources. Dalton Trans 2015; 44:15441-9. [DOI: 10.1039/c5dt02336j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We used halloysite, a nano-sized natural mineral and high surface area montmorillonite as supports for nano-sized Mn oxides to synthesize efficient water-oxidising catalysts.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
- Center of Climate Change and Global Warming
| | - Emad Amini
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan
- Iran
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42
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Hellmich J, Bommer M, Burkhardt A, Ibrahim M, Kern J, Meents A, Müh F, Dobbek H, Zouni A. Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal. Structure 2014; 22:1607-15. [DOI: 10.1016/j.str.2014.09.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/26/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
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43
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Wang L, Zhang C, Zhao J. Location and function of the high-affinity chloride in the oxygen-evolving complex – Implications from comparing studies on Cl−/Br−/I−-substituted photosystem II prepared using two different methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:249-55. [DOI: 10.1016/j.jphotobiol.2014.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/22/2014] [Accepted: 05/26/2014] [Indexed: 11/17/2022]
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44
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Najafpour MM, Heidari S, Amini E, Khatamian M, Carpentier R, Allakhverdiev SI. Nano-sized layered Mn oxides as promising and biomimetic water oxidizing catalysts for water splitting in artificial photosynthetic systems. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 133:124-39. [DOI: 10.1016/j.jphotobiol.2014.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/02/2014] [Accepted: 03/07/2014] [Indexed: 01/22/2023]
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45
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Singh DP, Khattar JIS, Gupta M, Kaur G. Evaluation of toxicological impact of cartap hydrochloride on some physiological activities of a non-heterocystous cyanobacterium Leptolyngbya foveolarum. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2014; 110:63-70. [PMID: 24759053 DOI: 10.1016/j.pestbp.2014.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 02/08/2014] [Accepted: 03/05/2014] [Indexed: 06/03/2023]
Abstract
The present study was aimed to the evaluation of toxicological impact of insecticide cartap hydrochloride on photosynthesis and nitrogen assimilation of a non-heterocystous cyanoprokaryote Leptolyngbya foveolarum isolated from paddy fields of Punjab, India. The microorganism tolerated commercial grade insecticide up to 80 ppm. Lower concentration (20 ppm) of cartap supported good growth with high dry weight of biomass, total protein content, photosynthetic pigments, photosynthesis and respiration compared to untreated control cultures while higher concentrations (40 and 60 ppm) inhibited these parameters in a dose dependent manner. Treatment of the microorganism with 60 ppm cartap lowered the content of photosynthetic pigments with maximum inhibitory effect on phycoerythrin (70% decrease) followed by allophycocyanin (66% decrease). Rates of photosynthesis and respiration were inhibited by 63% and 45%, respectively, while PS-I, II and whole chain activity were decreased by 45%, 67% and 40% respectively, compared to untreated control cultures. Cartap at 60 ppm decreased nitrate and nitrite uptake by 31% and 61%, respectively, whereas uptake of ammonium was slightly increased (18%) in cartap (60 ppm) treated cells. Nitrate and nitrite reductase, and glutamine synthetase activities of the microorganism decreased by 36-50% in 60 ppm cartap. The low levels of growth, photosynthetic pigments and activities of nitrogen assimilating enzymes in cells grown in nitrogen depleted medium supplement with insecticide indicated that insecticide may be used by the organism as a nitrogen source.
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Affiliation(s)
- D P Singh
- Department of Botany, Punjabi University, Patiala 147002, India.
| | - J I S Khattar
- Department of Botany, Punjabi University, Patiala 147002, India
| | - Meenu Gupta
- Department of Botany, Punjabi University, Patiala 147002, India
| | - Gurdeep Kaur
- Department of Botany, Punjabi University, Patiala 147002, India
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46
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Najafpour MM, Abasi M, Tomo T, Allakhverdiev SI. Mn oxide/nanodiamond composite: a new water-oxidizing catalyst for water oxidation. RSC Adv 2014. [DOI: 10.1039/c4ra06181k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein, we reported nanosized Mn oxide/nanodiamond composites as water-oxidizing compounds.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan, Iran
- Center of Climate Change and Global Warming
- Institute for Advanced Studies in Basic Sciences (IASBS)
| | - Mahnaz Abasi
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan, Iran
| | - Tatsuya Tomo
- Department of Biology
- Faculty of Science
- Tokyo University of Science
- Tokyo 162-8601, Japan
- PRESTO
| | - Suleyman I. Allakhverdiev
- Controlled Photobiosynthesis Laboratory
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow 127276, Russia
- Institute of Basic Biological Problems
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47
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Najafpour MM, Abbasi Isaloo M, Abasi M, Hołyńska M. Manganese oxide as a water-oxidizing catalyst: from the bulk to Ångström-scale. NEW J CHEM 2014. [DOI: 10.1039/c3nj01393f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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48
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Najafpour MM, Abasi M, Hołyńska M. Nanolayered manganese oxides as water-oxidizing catalysts: the effects of Cu(ii) and Ni(ii) ions. RSC Adv 2014. [DOI: 10.1039/c4ra05617e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We synthesized nanolayered manganese oxides in the presence of copper(ii) or nickel(ii) ions, and considered the water oxidizing activities of them.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan, Iran
- Center of Climate Change and Global Warming
- Institute for Advanced Studies in Basic Sciences (IASBS)
| | - Mahnaz Abasi
- Department of Chemistry
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan, Iran
| | - Małgorzata Hołyńska
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW)
- Philipps-Universität Marburg
- Marburg, Germany
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49
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Harms MJ, Thornton JW. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet 2013; 14:559-71. [PMID: 23864121 DOI: 10.1038/nrg3540] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality - the purviews of evolutionary biology and biochemistry, respectively - are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do.
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Affiliation(s)
- Michael J Harms
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
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50
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Ogata K, Yuki T, Hatakeyama M, Uchida W, Nakamura S. All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane. J Am Chem Soc 2013; 135:15670-3. [DOI: 10.1021/ja404317d] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Koji Ogata
- Nakamura
Laboratory, RIKEN Innovation Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Taichi Yuki
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Makoto Hatakeyama
- Nakamura
Laboratory, RIKEN Innovation Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Waka Uchida
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Shinichiro Nakamura
- Nakamura
Laboratory, RIKEN Innovation Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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